11 Result(s)

Article

Priority index for critical Covid-19 identifies clinically actionable targets and drugs

While genome-wide studies have identified genomic loci in hosts associated with life-threatening Covid-19 (critical Covid-19), the challenge of resolving these loci hinders further identification of clinically...

Zhiqiang Zhang, Shan Wang, Lulu Jiang, Jianwen Wei, Chang Lu… in Communications Biology (2024)

Article

Epigenomic analysis reveals a dynamic and context-specific macrophage enhancer landscape associated with innate immune activation and tolerance

Chromatin states and enhancers associate gene expression, cell identity and disease. Here, we systematically delineate the acute innate immune response to endotoxin in terms of human macrophage enhancer activi...

** Zhang, Harindra E. Amarasinghe, Justin P. Whalley, Chwen Tay… in Genome Biology (2022)

Article

Distinct immune signatures discriminate between asymptomatic and presymptomatic SARS-CoV-2^pos subjects

Increasing numbers of SARS-CoV-2-positive (SARS-CoV-2^pos) subjects are detected at silent SARS-CoV-2 infection stage (SSIS). Yet, SSIS represents a poorly examined time-window wherein unknown immunity patterns ma...

Shanhe Yu, Caixia Di, Shijun Chen, Mingquan Guo, Jiayang Yan, Zhaoqin Zhu… in Cell Research (2021)

Article

Integrating longitudinal clinical laboratory tests with targeted proteomic and transcriptomic analyses reveal the landscape of host responses in COVID-19

The pathophysiology of coronavirus disease 19 (COVID-19) involves a multitude of host responses, yet how they unfold during the course of disease progression remains unclear. Here, through integrative analysis...

Yun Tan, Wei Zhang, Zhaoqin Zhu, Niu Qiao, Yun Ling, Mingquan Guo… in Cell Discovery (2021)

Article

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

The Critical Assessment of Functional Annotation (CAFA) is an ongoing, global, community-driven effort to evaluate and improve the computational annotation of protein function.

Naihui Zhou, Yuxiang Jiang, Timothy R. Bergquist, Alexandra J. Lee… in Genome Biology (2019)

Article

An expanded evaluation of protein function prediction methods shows an improvement in accuracy

A major bottleneck in our understanding of the molecular underpinnings of life is the assignment of function to proteins. While molecular experiments provide the most reliable annotation of proteins, their rel...

Yuxiang Jiang, Tal Ronnen Oron, Wyatt T. Clark, Asma R. Bankapur… in Genome Biology (2016)

Article

A large-scale evaluation of computational protein function prediction

A report on the results of the first large-scale community-based critical assessment of protein function annotation (CAFA) experiment.

Predrag Radivojac, Wyatt T Clark, Tal Ronnen Oron, Alexandra M Schnoes… in Nature Methods (2013)

Article

A domain-centric solution to functional genomics via dcGO Predictor

Computational/manual annotations of protein functions are one of the first routes to making sense of a newly sequenced genome. Protein domain predictions form an essential part of this annotation process. This...

Hai Fang, Julian Gough in BMC Bioinformatics (2013)

Article

An organogenesis network-based comparative transcriptome analysis for understanding early human development in vivo and in vitro

Integrated networks hold great promise in a variety of contexts. In a recent study, we have combined expression and interaction data to identify a putative network underlying early human organogenesis that con...

Hai Fang, Wen **, Ying Yang, Ying **, Ji Zhang, Kankan Wang in BMC Systems Biology (2011)

Article

The evolutionary dynamics of protein networks

Hai Fang, Julian Gough in Genome Biology (2010)